BioC 3.5: CHECK report for bioassayR on malbec2
This page was generated on 2017-08-16 13:15:19 -0400 (Wed, 16 Aug 2017).
bioassayR 1.14.0 Tyler Backman
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/bioassayR | Last Changed Rev: 129126 / Revision: 131943 | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
Summary
Package: bioassayR |
Version: 1.14.0 |
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings bioassayR_1.14.0.tar.gz |
StartedAt: 2017-08-15 21:28:21 -0400 (Tue, 15 Aug 2017) |
EndedAt: 2017-08-15 21:29:33 -0400 (Tue, 15 Aug 2017) |
EllapsedTime: 71.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: bioassayR.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings bioassayR_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/bioassayR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bioassayR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bioassayR’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bioassayR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
bioassayR.Rcheck/00install.out:
* installing *source* package ‘bioassayR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘organism’ in package ‘bioassayR’
Creating a new generic function for ‘organism<-’ in package ‘bioassayR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bioassayR)
bioassayR.Rcheck/bioassayR-Ex.timings:
name | user | system | elapsed
|
BioAssayDB-class | 0.000 | 0.000 | 0.001 |
|
activeAgainst | 0.172 | 0.004 | 0.175 |
|
activeTargets | 0.032 | 0.000 | 0.032 |
|
addBioassayIndex | 0.004 | 0.008 | 0.011 |
|
addDataSource | 0.028 | 0.000 | 0.027 |
|
allCids | 0.004 | 0.000 | 0.004 |
|
allTargets | 0.004 | 0.000 | 0.003 |
|
assaySetTargets | 0.096 | 0.008 | 0.106 |
|
bioactivityFingerprint | 0.196 | 0.004 | 0.201 |
|
bioassay-class | 0.024 | 0.000 | 0.024 |
|
bioassaySet-class | 0.000 | 0.000 | 0.002 |
|
connectBioassayDB | 0.012 | 0.000 | 0.012 |
|
crossReactivityProbability | 0.256 | 0.004 | 0.260 |
|
disconnectBioassayDB | 0.004 | 0.008 | 0.010 |
|
dropBioassay | 0.124 | 0.000 | 0.123 |
|
dropBioassayIndex | 0.012 | 0.004 | 0.018 |
|
getAssay | 0.012 | 0.000 | 0.014 |
|
getAssays | 0.040 | 0.000 | 0.041 |
|
getBioassaySetByCids | 0.120 | 0.000 | 0.123 |
|
inactiveTargets | 0.004 | 0.000 | 0.006 |
|
loadBioassay | 0.180 | 0.004 | 0.182 |
|
loadIdMapping | 0.008 | 0.000 | 0.008 |
|
newBioassayDB | 0.008 | 0.000 | 0.006 |
|
parsePubChemBioassay | 0.008 | 0.000 | 0.009 |
|
perTargetMatrix | 0.148 | 0.000 | 0.151 |
|
queryBioassayDB | 0.016 | 0.004 | 0.017 |
|
samplebioassay | 0.000 | 0.000 | 0.002 |
|
scaleBioassaySet | 0.020 | 0.000 | 0.022 |
|
screenedAtLeast | 0.004 | 0.000 | 0.008 |
|
selectiveAgainst | 0.060 | 0.000 | 0.064 |
|
targetSelectivity | 0.088 | 0.000 | 0.091 |
|
translateTargetId | 0.012 | 0.000 | 0.009 |
|
trinarySimilarity | 0.144 | 0.000 | 0.143 |
|